Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_011424894.1 RHE_RS08000 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >NCBI__GCF_000092045.1:WP_011424894.1 Length = 310 Score = 498 bits (1281), Expect = e-146 Identities = 247/310 (79%), Positives = 272/310 (87%) Query: 1 MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD 60 M PKIFIDGEHGTTGLQIR RMAGR D+ELLSIPEAERRNAAMRED+LNSADIA+LCLPD Sbjct: 1 MAPKIFIDGEHGTTGLQIRTRMAGRRDVELLSIPEAERRNAAMREDMLNSADIAMLCLPD 60 Query: 61 DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120 DAS+EAV MV+ NN VR+IDTSTA RV P WAYGFAEMDK Q ++I AR V+NPGCYPT Sbjct: 61 DASKEAVQMVSANNNVRVIDTSTAFRVNPGWAYGFAEMDKEQAEKIASARFVSNPGCYPT 120 Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180 GAI LIRPLR AGILPDGYPVTVNAVSGY+GGGKQMIAQME+ +PD I APHFLYGL L Sbjct: 121 GAIGLIRPLRAAGILPDGYPVTVNAVSGYSGGGKQMIAQMENPDHPDAITAPHFLYGLPL 180 Query: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240 HKHVPEM +HGLL+RAP+FSPSVGKFAQGMIVQVPL+L+DLA G T+E+IH ALV HYA Sbjct: 181 THKHVPEMTVHGLLDRAPIFSPSVGKFAQGMIVQVPLHLDDLAEGTTMESIHAALVAHYA 240 Query: 241 GQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAA 300 GQ IV VVPL +S LAR++A EL G D MKLFVFGT GG+ VNLVALLDNLGKGASGAA Sbjct: 241 GQEIVTVVPLSDSKALARVNAVELEGKDTMKLFVFGTPGGSQVNLVALLDNLGKGASGAA 300 Query: 301 VQNMDLMLSA 310 VQNMDLML++ Sbjct: 301 VQNMDLMLAS 310 Lambda K H 0.319 0.136 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 400 Number of extensions: 12 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 310 Length of database: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_011424894.1 RHE_RS08000 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01851.hmm # target sequence database: /tmp/gapView.8429.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01851 [M=310] Accession: TIGR01851 Description: argC_other: N-acetyl-gamma-glutamyl-phosphate reductase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-131 423.3 0.0 3.3e-131 423.2 0.0 1.0 1 lcl|NCBI__GCF_000092045.1:WP_011424894.1 RHE_RS08000 N-acetyl-gamma-gluta Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011424894.1 RHE_RS08000 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.2 0.0 3.3e-131 3.3e-131 1 308 [. 2 308 .. 2 310 .] 0.98 Alignments for each domain: == domain 1 score: 423.2 bits; conditional E-value: 3.3e-131 TIGR01851 1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 +pk+fidGe GttGlqir r+a+r d+ellsi e r++a+ r ++ln+ad+a+lclpdda++eav +v lcl|NCBI__GCF_000092045.1:WP_011424894.1 2 APKIFIDGEHGTTGLQIRTRMAGRRDVELLSIPEAERRNAAMREDMLNSADIAMLCLPDDASKEAVQMV 70 69*****************************************************************99 PP TIGR01851 70 d.npntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadf 137 + n+n++++d+sta+r++++w+yGf+e++ eq ekia+a++v+nPGcy+tgai l+rPl +aGilP + lcl|NCBI__GCF_000092045.1:WP_011424894.1 71 SaNNNVRVIDTSTAFRVNPGWAYGFAEMDKEQAEKIASARFVSNPGCYPTGAIGLIRPLRAAGILPDGY 139 747889*************************************************************** PP TIGR01851 138 PvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfa 206 Pvt+navsGysGGGk++ia+ e+ d+ +a+++ ygl l+hkh+pem++h+ l + Pif P+vG+fa lcl|NCBI__GCF_000092045.1:WP_011424894.1 140 PVTVNAVSGYSGGGKQMIAQMENPDHPDAITAPHFLYGLPLTHKHVPEMTVHGLLDRAPIFSPSVGKFA 208 **********************99999999*************************************** PP TIGR01851 207 qGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvf 275 qG++v++plhl +l++ ++ e ih+al+ +y+G++ v v++l+d+++l ++a l+g ++++lfvf lcl|NCBI__GCF_000092045.1:WP_011424894.1 209 QGMIVQVPLHLDDLAEGTTMESIHAALVAHYAGQEIVTVVPLSDSKAL--ARVNAVELEGKDTMKLFVF 275 ************************************************..8899999************ PP TIGR01851 276 gsddgerallvarldnlGkGasGaavqnlnial 308 g+ g ++ lva+ldnlGkGasGaavqn++++l lcl|NCBI__GCF_000092045.1:WP_011424894.1 276 GTPGGSQVNLVALLDNLGKGASGAAVQNMDLML 308 ********************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (310 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.60 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory